Chuck & Sarah vs The Butterfly Effect
by TheKyrien
Summary: People always wonder "what if?", would things have been different? Chuck and Sarah's story was always meant to be but what happens when those close to them make choices that change their beginning, middle and end? AU with cannon references. Firmly Charah.
1. Choices Made, Part One

**A/N:** First off, I'd like to thank you for reading. Secondly, I'm taking quite a few liberties with the timeline because a lot of events were only hinted at happening. I am also disregarding a few dates that are as established as cannon, factual or not, which may or may not be apparent tor readers. Also, this has been proof-read but hasn't been beta'd since I do not have one. All mistakes are my own. That said, enjoy.

**Disclaimer:** I do not own Chuck.

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><p><strong>Chapter One: Choices Made, Part One.<strong>

**August 1998**

The door opened silently on the well oiled hinges and he peered carefully through the doorway, being caught now would completely ruin his plan. Seeing the target lying prone, he let out the breath he hadn't even realized he was holding. She was still out cold.

Inching forward, he made certain to continue aiming at the target, moving slowly to avoid rousing her. He leaned forward, angling his hands towards her upper torso, ready to dispense with the package.

"I know you're there Dad, I heard you opening the door."

Jack Walker was not what one would consider a young man and the sudden voice of his daughter caused him to yelp and stumble a bit. Catching himself before he emptied the package all over the floor, he took a deep breath to balance himself.

"You shouldn't be doing that to your old man, Darlin'" Jack said as his daughter turned her face towards him, a single hooded blue eye regarding him stonily. She really was not a morning person.

"And my 'old man'," she deadpanned, using her fingers to make air quotes. "Should not be creeping into his teenage daughter's bedroom while she's sleeping! And he most certainly should not be waking her up at the crack of dawn!"

Smiling slowly, Jack placed the tray in her lap as she pulled herself into a sitting position.

"It's your first day of school in your senior year, I thought I'd make you something special. Your favorite french toast, whipped cream, fresh strawberries... Just how you like it."

Her eyebrow quirked upwards as she regarded him with amusement, becoming more alert by the second. "I'm not twelve anymore, Dad."

"Well, you need to eat something, big day at school. You only attend senior year once, you know. So finish your breakfast and get ready for school, you're supposed to pick up the schnook in thirty minutes." He said, ducking out of her room, narrowly avoiding the pillow she had tossed at him.

"He's not a schnook, he's my best friend!"

She never did like him calling her best friend a schnook.

"Whatever you say Darlin', he's still a Class A schnook." Jack called as he headed downstairs.

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><p>Jack looked up from his paper when he heard footsteps rapidly descending the staircase and saw his daughter zip right by him to deposit her dishes in the sink before heading over to him.<p>

"Love you." she mumbled as she pressed a quick kiss to his cheek before rushing out towards the garage.

"Love you too." he said, the dull thud of the front door slamming shut his only answer. Standing up, he walked over to the open door and called out to Sarah as she started her car. "See you later, alligator."

Her hand appeared over the the top of her pulled down hood as she pulled out of the driveway and made a left, away from the house at a speed that was not technically safe.

He grinned to himself, shaking his head in mild amusement at his baby girl's intense dislike for mornings and her near chronic tardiness.

As the morning dragged on, Jack found himself focusing less on the paper he still held in front of him and more on his thoughts. As it always did during the quiet hours when he was alone, Jack reflected on key events in his life; his wedding, the birth of his daughters; the day he took Sarah away from her grandmother and, as his thoughts always wandered to during his time of introspection, the day he met the person who changed his life, forever.

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><p><strong>February 1992 – Madison, Wisconsin.<strong>

"Welcome back to Science, Here and Now. We're joined this hour by Dr. Penelope Queen from the physics department at M.I.T. Welcome Dr. Queen."

"Thank you Cooper, it's a pleasure to be here."

"So tell us Dr. Queen, we've been hearing a lot recently about 'The Butterfly Effect', could you explain to our listeners exactly what this effect is all about?"

"Absolutely Cooper, 'The Butterfly Effect' is, depending on who you ask, a part of chaos theory that, at the very core, is about cause an effect. The name comes from the idea that a butterfly flapping its wings somewhere could effect a huge change on weather somewhere else."

"That's fascinating but how does that actually relate to our lives?"

"Well, this is where it gets interesting. The notion that I just presented you is probably the least technical definition of 'The Butterfly Effect.' Think about it this way. The end result of something huge is impacted by the beginning. If A had happened instead of B, what would the end result look like?"

"Hold that thought Dr. Queen, we have to go to comm..."

The buzz of the radio died down briefly as Danny O'Connell spun the dial to change to another station before jumping back to fill the interior of the car with a catchy tune.

Danny glanced into the rear view mirror and spied his not-quite-eleven year old daughter dozing in the back seat. He was a bit conflicted, pulling this last job in Wisconsin before moving on to Ohio but he could use the extra money.

It was a simple enough job, he rationalized. Pose as a lawyer, promise a client something or another, and run off with a nice down-payment that would keep him afloat till his next job. Simple.

Taking a left on the next corner, Danny spied his destination just over a block down the road. The tan walls of hotels where the meeting was supposed to take place rising higher than its neighbors, the windows reflecting the midday sun.

Making sure to leave a note where Katie would find it, Danny locked the car doors and headed up to the bar and attached lounge. He straightened his tie and smoothed over his mustache one more time before stepping into the elevator.

A quarter of an hour later and he was getting annoyed but he pushed down his emotions. After all, in his line of work, patience was the ultimate virtue. Downing the last of his drink, he motioned for the bartender to refill it but was interrupted by a voice.

"Mr. O'Connell, I presume?"

Danny turned around quickly, startled by the sudden voice. He was met humorless chuckle that sent a slight chill up his spine.

"I'm sorry to have startled you Mr. O'Connell," the man speaking to him said. "My name is Greg Tuttle."

For some reason, the first thought that popped into Danny's mind was "This guy could've played James Bond." Shaking off the random thought, Danny decided it was time to turn on the charm. "Pleasure is mine, Mr. Tuttle and please, call me Danny."

"As you wish Danny," Tuttle replied, taking a quick look around their surroundings. "Perhaps it will be prudent to move our discussion to a more... Private venue?"

"Of course, of course, I reserved a booth for us. If you'll just follow me."

A few minutes after they were seated in the booth and after having exhausted all forms of pleasantries, Tuttle cleared his throat loudly before leaning forward just a bit.

"Now, Mr. O'Connell," he began.

"Please, like I mentioned, call me Danny. I hear someone say Mr. O'Connell and I find myself looking over my shoulder for my father."

"As you wish, Danny. The reason I need your services is because I am looking to expand my business out here, to the United States and I find myself in need of someone taking caring of those bothersome applications and permits."

"I'm not a boastful man, Mr. Tuttle, but I can assure you that I am very good at what I do. I just need a bit more detail... We should also discuss me fee."

"Do this for me and I'll be glad to pay whatever you are asking, within limits of course."

"Of course."

The technical aspects of the business deal dragged on for another half hour or so. The basic of it all was Tuttle owned a shipping and courier company in his homeland and he was looking to open up his first office in the United States.

Danny was expected to handle all the documentation that would be needed as well as any details that had to be sorted out with the government.

Smiling slightly, Tuttle pulled out a bulging envelope from his coat pocket and pushed it across the table towards Danny as the discussion drew to a close.

"All the information you need is inside including a down-payment of fifteen thousand dollars and here is my card. I'll be in town for a few more days and you can reach my at anytime at this number on the back." Tuttle said as he stood up and buttoned his business coat.

"I can have an update for you within the week, Mr. Tuttle." Danny replied, standing up as well and reaching his hand forward. "I'm looking forward to a mutually beneficial relationship with you and your company."

Tuttle looked straight into Danny's eyes for a moment and, for the briefest of seconds, Danny felt a nervousness he couldn't explain. After all, he was a professional and had done this dozens of times before.

The moment passed when Tuttle smiled and took Danny's hand in a hearty shake and left.

Slipping the envelope Tuttle had given him into his coat pocket, Danny made his way slowly to the elevators, giving Tuttle more than sufficient time to have left the area.

Getting into his car, he saw that Katie was just beginning to stir, never even noticing she had been left alone for just over an hour. Undoing his tie and pulling off the fake mustache, Danny waited for Katie to fully wake before turning to her.

"Well Darlin', I'm all done with work here. What say you and I relax for a couple of days before heading on down to Ohio?"

"I thought you said we shouldn't hang around once we're done working, Daddy?"

Katie was right, of course. They should be heading down to Ohio before Tuttle learned that the so-called lawyer he had met didn't exist. Danny had also arranged a meet with his next mark, a wealthy widow who was looking to liquidate some assets post haste.

Still, Danny figured he had bought them at least a week of leeway with Tuttle and his meeting with the widow wouldn't be for another two days and, as he always said...

"Now Katie, a good conman c..."

"Can leave whenever he wants, I know daddy."

"So what say you and I pick up dinner and head on back to the motel to watch some T.V.?"

Katie's eyes brightened as a toothy grin slowly spread across her face. She rarely got to enjoy the simple pleasures of life, being on the road as often as she was with her father and, if she played her cards right, she might just get a little extra as well. "Only if we get some ice cream too!"

"Of course Darlin'." Danny drawled, smiling a little at her request. She was learning fast.

Her grin blossomed into a full-on smile as Danny started the engine.

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><p>A couple of hours later, Danny was perusing the files he had received from Gregory Tuttle, taking notes in a shorthand that few would be able to read on a yellow legal pad.<p>

He rolled his shoulders, the stiffness building after hunching over a bunch of papers for such a long period of time.

"Time well spent," He muttered to himself. He had found a couple of avenues that he could proceed with for future cons and some of the credentials provided with the documentation would help in the creation of future identities.

Taking a short break from the documents, he once again considered making the trip down to Ohio. After all, it was a relatively long drive and he did have the "business meeting" in a couple of days. The documents also weren't going anywhere and he'd have more time later to mull over its contents.

Turning to look at the bed, he saw his daughter sound asleep. Shrugging his shoulders in resignation, Danny went over to tuck her in before pulling on his coat, deciding to take a brief stroll to process the information he had gleaned from Tuttle's documents. He would wake her up first thing in the morning and they would drive down to Columbus then. He smiled to himself as he imagined the fuss Katie would almost certainly make at having to wake up early. Maybe he would just carry her to the car and let her continue to sleep, he thought.

Locking the door behind him, Danny swung his arms up, stretching out the muscles before heading to the entrance of the motel lot.

As he took a right down the street, parallel to the motel, he never saw the dark gray sedan parked across the road or the brunette dressed in white shirt and black cardigan jacket watching him.

_To be continued..._

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><p><strong>AN:**Kudos to the people who can pick up the references to the different episodes and to other shows. Chuck and Sarah won't show up for a couple of chapters yet, but it will get there, I promise. I should also say that I am in no way involved in the study of physics so I am actually unclear on whether my explanation of the Butterfly Effect is accurate but that is how I interpreted it, I apologise if it is not actually clear. Cheers.


	2. Choices Made, Part Two

**A/N:** Thank you to the people who reviewed and who read. Due to the lack of information, I have also decided to take a few liberties with names as well. As before, I have no beta so all mistakes are my own.

**Disclaimer**: I do not own Chuck.

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><p><strong>Chapter Two: Choices Made, Part Two.<strong>

**February 1992.**

Danny was right, Katie did make a fuss about being woken up at six in the morning. An awfully loud and extremely trying fuss. It was only through judicious use of bribery that he had eventually managed to get her to quiet down. A small respite but a respite none-the-less, her displeasure still wholly evident. Even now, she sat rigidly in the backseat, her arms comically crossed in front of her as she stared furiously ahead, her lips pursed in a demanding pout. The look on her face promised a continuation of the earlier tantrum if her demands were not met soon.

And her demands were simple, really, only two words. "Chocolate croissants," she had said.

Danny grimaced as he got back into the car after the second stop that bore no fruits in the search for Katie's demands. Objectively, he knew it would be hard to find chocolate croissants at, he glanced quickly at his watch, ten minutes before eight in the morning but his little girl brooked no excuses. Maybe he had trained her on how to work a mark a bit too well.

Four stops and nearly forty minutes later, Danny nearly did a victory dance when he spotte the illusive French pastry on a tray. Walking out from the bakery holding a bag of fresh chocolate croissants, Danny watched as Katie's eyes lit up, her frown smoothed out and her pout disappeared in the span of half a second. He began to frown himself since he was now almost certain that Katie had played him. Or was she that enamored with chocolate croissants? A question he was almost certain he would never get the answer to.

"So by your leave, princess," Danny said, twirling his hand with a flourish after he had gotten into the car. "I would like to begin our trip to Columbus now."

The reply he got was nothing more than soft chewing sounds and a slight nod of her head.

The drive itself was about what Danny had expected, the radio's crooning battling against the thrum of the engine and the whipping of the wind rushing by. Roughly three hours since the trip proper that Katie insisted on a stop, her constant badgering convincing Danny that maybe a bit of a breather would do them both a world of good.

Stopping at the next gas station he spotted, Danny left Katie to her own devices for a few minutes while he popped into the small attached convenience store to pick up a some water and maybe a few bags of potato chips, anything to keep Katie occupied during the remainder of the trip. As he made his way towards the cashier, his eyes wandering over the customers, Danny walked straight into a thirty-some-year-old woman dressed smartly in a business suit, making her spill the cup of coffee she clutched in her hands all over his white shirt.

"Oh my goodness, I am_ so_ sorry!" the woman gushed as she fumbled in her purse for something to help soak up the coffee.

"It's okay, part of this," Danny gestured at the mess on his shirt. "Is my fault, I should've been paying more attention to where I was going."

"Regardless, I'm so terribly sorry mister..." the woman faltered, eyes questioning as she held out a white handkerchief.

"Franco," Danny replied, slipping into the identity that he had prepared for Ohio. "James Franco."

"Well Mr. Franco, let me say again how sorry I am for this. If you're going to be in Madison anytime soon, I'd be glad to pay for your dry cleaning."

"That's terribly kind of you but I'm headed down to Ohio myself, family recently moved there."

"Of course, of course," she murmured. "Well, let me give you my card and if you ever find yourself in Madison again, don't hesitate to drop me a message, I'd feel terrible otherwise."

"Certainly miss..." Danny paused, looking down quickly at the business card the woman had pressed into his hand. "Rimes. Tell you what, if I ever make it back up to Madison, we can go grab a cup of coffee to make up for this entire mess."

"That sounds perfect." she smiled before her eyes widened and she grabbed his left hand, raising it to her eyes. Danny was caught by surprised at the sudden action but was filled with understanding as he saw the woman looking at his watch.

"Oh goodness, I'm so sorry to leave you like this but I'm really late! I was already running behind but then this happened and I'm supposed to be checking in with the office soon and there's this meeting that..."

"It's perfectly fine Ms. Rimes, you go on ahead while I go get cleaned up."

"Thank you so much Mr. Franco and once again, I'm so sorry!" she called out as she moved quickly to the exit. Danny watched on in amusement at the woman as she scrambled into a gray sedan and a few seconds later, the ignition sounded and the car pulled out of the station.

Making his way to the cashier, Danny paid up for his purchases as well as asking where the restroom was. The clerk took one look at the large stain on his shirt and mutely jerked his thumb behind him, indicating the hanging sign outside that said, in bold print, restrooms.

Making a quick detour to check up on Katie, who was aimlessly walking up and down the front of the store, Danny handed her his purchases with instructions to wait in the car. Katie nodded her understanding as he made his way to the restrooms to clean up.

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><p>"Yes, that's what he said, moving to Ohio for family reasons.<p>

"No, no mention of an O'Connell at all.

"I'm absolutely certain it was him.

"Of course I wasn't made, that's a rookie mistake.

"Are you accusing me of something?

"Terminate him? Yes, Mr. Volkoff, I understand. I'll wait for your call before following through with the termination."

Taking a deep breath and exhaling, Martha Rimes, as she was presently known to the state of Wisconsin, pushed the off button on the bulky wireless phone she had used to contact her _employer_. She hated this part of the job, some innocent... well, _mostly_ innocent... person getting caught in the crossfire and she had no choice but to get rid of them lest suspicion fell upon her. She was one of the good guys, for goodness' sake, and she hated this part of her mission.

It had all started five years ago.

Martha Rimes was widely acknowledged as one of the most promising phantoms in the CIA. No one knew who she really was or what she really looked like. It helped that her assignment for the past few years had been a long term, deep cover assignment.

It was a day like any other when she received the coded missive straight from the office of the Deputy Director of Operations. Eyes only, codeword and **well** above top secret. She was still relatively young at that point and had jumped at the opportunity. It was only after her briefing that she realized exactly what she had gotten into; deep undercover inside a paramilitary arms organization that had a lot of very powerful people sweating.

The mission itself was not entirely out of the ordinary except it clashed horribly with her current assignment and the name of the key target in the new mission was someone her partner had been trying, without any success, to flag as a threat. Her partner was one of the best in the business but when confronted with an army of CIA analysts who claimed there were no reasons to worry, her partner's concerns had been dismissed.

_And now it's coming back to bite **me** in the ass_, Martha thought. She wondered if part of the reason she was chosen was because of the information her partner had amassed about this new organization.

The mission parameters were, initially, acceptable. Short term assignments through Volkoff Industries, it's always the Russians she had thought at the time, that would keep her away from her partner for a few days to weeks at a time. She served whatever purpose Volkoff Industries needed her for, be it messenger, courier, mediator or assassin and she was fine with it since, more often than not, the people she was ordered to kill were absolute scum.

It was only now that she had worked her way up the ladder that Volkoff had taken an interest with her. He rarely allowed members of his organization to travel with him directly but Martha had escorted Volkoff from Heathrow to Mitchell International in Milwaukee before the hour or so drive to Madison. The one thing that she had not expected from Volkoff were his subtle inquiries into her past. Whether he was making direct inquiries or not, she was not sure but trusted in both the CIA and her partner to keep cover intact.

Shaking herself out of memory lane, Martha prepared herself for what she had to do. Terminating James or Danny or whoever he really was would be her last resort. She was sure she could convince her bosses that WitSec might be a more appropriate choice or maybe...

Starting up the engine of her red Lotus Elan, she pulled out a much smaller wireless phone and pressed the number one, waiting for the device to connect her to her partner.

"Orion, secure."

"Frost, secure."

"I was starting to get worried about you." her partner said. "And what is that sound?"

"It's just the car, honey. I'm sorry I haven't been in touch, I've had company until fairly recently."

"It's okay, just missing you. When are you coming back?"

"Soon as I get this over and done with, which is one of the reasons I called. I need your help locating a mark, a James Franco, known aliases include Danny O'Connell. Any information you might have on him will also be helpful."

"I'll get right on it."

"And..." Martha faltered, wondering if it was a good idea.

"And?"

"... Prepare a Protocol Two on James Franco."

"Protocol Two? Are you sure?"

"I think so, I'm not entirely comfortable with the present situation but this might help some."

"All right, I'll go ahead and get started then. I'll get his location to you through the usual channels, check on it tomorrow."

"Okay, love you and I'll see you soon... Tell the kids I love them."

"Love you, too and I will. Now go catch some bad guys and make me proud."

Smiling to herself, Martha pressed the disconnect button on her mobile phone and stashed it away in a hidden compartment of her purse. Shifting the Elan into gear, she slipped on her Matsuda 2809 sunglasses and took off down the roar with a mighty roar of the engine.

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><p>James Franco arrived with his daughter, Rebecca, in Columbus, Ohio, late in the afternoon and the first order of business was checking in to their hotel. He had decided to splurge a bit and go for an actual hotel instead of the usual motels by the freeways and so far, he was loving it. There was no denying that the just over double price he had paid resulted in a less seedy environment and the beds seemed a bit softer, the sheets a bit more crisp and the sound of cars... What sound?<p>

There was also a more practical reason for choosing a safer base of operations while staying in Columbus. His business dealing with the widow would necessitate his absence for long periods of time over the next few days and he was not going to be able to bring Rebecca along with him. Leaving her alone in a less than reputable place just spelled trouble. Speaking of Rebecca...

Having been the in the car for almost ten hours had her restless and fidgety. Figuring a good way to burn off the energy she had built up from the ride would be a walk to a nearby restaurant for dinner, rather than another car ride, he made her slip on a jacket before heading our the door.

The meal was pleasant and the walk seemed to exorcise the restlessness out of Rebecca, for which James was especially glad. Rebecca was fairly temperamental and leaving her energy bottled up till bed time would mean a fight of truly epic proportions.

After getting back to their hotel room, James proceeded to draw a bath for Rebecca. He was certain a nice long soak in a bubble bath would help her slip into a more relaxed state and would therefore mean less work when he tried to get her to sleep. This was a pattern that always followed their long inter-state trips and the bubble bath method was the surest that he had.

Once Rebecca was asleep, James made his way to his bag to extract the folder full of documents Tuttle had handed to him. Picking up where he had left off the previous night, James continued on his search for useful bits of information that he could use for future cons.

James was so wholly engrossed in the documents and his notes that he never realized how late it had gotten. He bit back a curse when he glanced at the his watch and saw that it was well after two. _Damn it_, he thought, _meeting in the morning and I choose tonight to get caught up in other things_.

Deciding that it was far too late to worry about it, James called the front desk to make sure they'd call him in the morning so he could make the meeting. First night in town and he was already off on the wrong foot. His last thought before clicking out the lights was _I sure hope I get out on the right side of bed._

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><p><em>All in all, that went rather well<em>, James thought smugly. He had made it to the meeting, barely, and had survived making small talk with a trophy wife who had been eagerly counting down to her late and **much** older husband's demise to cash in and her good fortune would be James' great fortune. He had already managed to earmark an expenses account from the widow while he "liquidated" their assets.

He was whistling to himself as he stepped into the lobby of his hotel, figuring Rebecca could entertain herself for another hour or so while he went to the bar to get himself a congratulatory drink. Two big scores in three days was a new record for him.

While James sat at the bar, waving for the bartender's attention, Martha watched him from across the attached lounge, stealthily ensconced in a booth shrouded in deep shadows. Martha was certain she was applying more caution than warranted since she was almost positive that even if James could see her, he almost certainly would not recognize her. It was amazing what a simple blonde wig, glasses and a slight altering of her posture could do to mask her identity. _Still, being cautious never hurt anyone_, she figured.

She had picked up the local newspaper early in the morning and had immediately turned to the classifieds section. Her partner had come through for her, as always, using a predetermined cipher to encode the mark's hotel, room number and real name. The little "missing you much" at the end was also a welcome addendum.

Now sitting here, watching him nurse what looked like whiskey, she was wondering whether this sleaze was worth saving. She wasn't entirely certain on the details but she knew that he had just returned from smooth talking his way into the bank account of a recently widowed woman. The fact that she had been ordered to potentially terminate Danny O'Connell most certainly did not help his cause. She had a cover to maintain, after all.

Martha made her way to the stairwell and climbed the few flights of stairs between the lobby and the floor James' room was on. She figured that since the hotel was equipped with a couple of elevators, the stairwell would be relatively unused and a good place to keep watch on James' room.

As she sat against the door of the stairwell a couple of hours later, her large bulky Roark Instruments mobile phone started to ring. Answering it quickly as the sound reverberated through the empty stairwell, the two words she had been expecting to hear was the only greeting she got. "Kill him."

Volkoff sounded angry and she suppose she understood why. If there was one thing that she had learned in the five years working for Volkoff Industries it was that Alexie Volkoff did not take being played for a fool well, not at all. There were many a horror stories that abounded within the organization of how Volkoff would summarily execute anyone, on the spot, who dared to speak out of turn or embarrass him in any way, often with their own weapons.

Sighing to herself, she figured a quick bullet between the eyes would solve the problem of the day. _Looks like Protocol Two won't be needed after all_, she thought. Pulling out the silencer for her beretta and slowly screwed it on. Just to be sure, she'd wait another few hours before proceeding with the hit; the late hour would ensure a much lower chance of anyone stumbling upon her in the act.

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><p>Martha had ended up waiting till after midnight, just in case, before exiting the stairwell and making her way to the mark's room. Pulling her beretta out of her purse and stuffing it in her coat pocket, she peered up and down the corridor, just to be certain that no wayward guests would play witness to the hit.<p>

Once she was satisfied that there was no one around, she crouched in front of the door and thanked her lucky stars that the hotel they were in had not yet transitioned to the newer key cards. Breaking through one of those without her partner around would have been a nightmare. She peered through the gap at the bottom of the door just to make sure there was no movement in the room before swiftly picking the lock.

Martha cringed slightly when the door swung open, making an almighty creaking sound. Holding her breath, she peered inside carefully, looking for any signs of movement or alarm.

When she was satisfied that no one had been awoken because of the sound, she crept into the room and slowly, very slowly, closed the door. Once she was satisfied that there would be no further interruptions to her mission, Martha strode forwardly confidently, the carpet muffling the heavy footfalls of her heeled boots.

Raising her gun, she strode out of the short corridor that preceded the room proper and... faltered. She saw two beds and a lump underneath the sheets of each one. Martha frowned. She had followed the mark for three days, how had she not noticed aother person with him.

A sudden rustling from the bed closest to her caused her to quickly train the barrel of her gun on the moving lump. When a little girl popped out from underneath the covers, Martha's mouth fell open in complete surprise.

_How the **HELL** did I miss that? _She thought to herself as the little girl rubbed her eyes a little before ambling forward a step. Martha had a second to decide on a course of action but the surprise at seeing the little girl cost her preciously.

"Daddy!" the girl shrieked when she noticed Martha in the room, instantly jolting her father awake.

_Damn it, damn it, damn it!_ Kept running through Martha's mind as she trained her gun on James Franco.

It took a couple of seconds for his mind to catch up to the images his eyes were sending it. When realization seeped through his sleep muddled thoughts, he quickly leaped out of bed and in front of Rebecca, assuming a placating stance. Maybe he could talk his way out of this.

"Look, whatever it is you want, I'm sure we can come to some kind of understanding." he said, trying to inject as much calmness as he could into his voice while pointing towards the desk that held a few envelopes full of cash. "There's twenty thousand there, just take it and we can all forget this ever happened."

Martha's mind was racing a mile a minute as she processed all the information she had. There was absolutely no way she could execute this man in front of his daughter. Hell, she doubted it was in her to execute him at all now that she knew James had someone who depended on him.

_I guess that means I go with Protocol Two._

Lowering her gun a bit, Martha ripped off the blonde wig, took off the glasses and straightened her posture. She could literally see the moment realization entered James' eyes.

"Martha Rimes?"

Resolving on following through with her alternate plan, Martha took a deep breath before answering him.

"I'm Special Agent Mary Frost of the CIA, Mr. Burton. There are many things we need to discuss."

At the words CIA, James' eyes had gone wide. When he heard his real last name, James was beyond shocked and looked to be on the verge of having a panic attack.

Mary took in the stunned look as a sort of wildness entered his eyes. _Yup,_ she thought, _he's definitely panicking._ Rubbing her temples with the hand not holding the gun, she said to James.

"Don't freak out."

_To be continued..._

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><p><strong>AN: **Once again, kudos to whoever can figure out the multiple references (not very well) hidden in the story. Also, when deciding on the name James Franco, I honestly had no idea that he was an actor until I decided to suddenly Google the name. Please let me know if you spot any glaring errors. As I said, I'm doing this alone and my eyes can only pick up so many errors. Thanks


	3. Choices Made, Part Three

**A/N: **Thanks to everyone who read and reviewed. Still no beta or even a second set of eyes so please excuse any and all grammatical and spelling mistakes. My eyes glaze over a bit when I'm reading this for the fifteenth time so I'm no longer able to pick out the small errors. Also, for those who read **vs. the Reassignment **and wanted more, please read the notes at the end of this chapter, thanks.

**Disclaimer: **I do not own Chuck.

* * *

><p><strong>Chapter Three: Choices Made, Part Three.<strong>

**February 1992, Columbus Ohio.**

James watched Special Agent Mary Frost of the CIA pace in front of him with wide eyes. For what seemed like the millionth time in the last hour, he reached one hand over to the other and pinched himself. Convinced that he was, indeed, not dreaming from the slight twinge in his left hand, James once again thought back to the increasingly rapid tailspin of events that had occurred once Agent Frost had started explaining his situation.

He had apparently conned a very, very dangerous man named Alexei Volkoff who was wanted not only by the United States government but many other countries around the world for providing arms to various organizations and political factions that had no business being in possession of vasts arrays of weaponry. The fact that this man was seeking to expand his network into the United States had yet to be picked up by the various intelligence agencies and that made James an even bigger target.

Owing to the fact that Volkoff hadn't yet figured out that Frost was a mole in his organization, the simple fact that James had seen fit to con him and run meant that James was the only known person alive that was outside Volkoff's sphere of influence. The fact that James had knowledge of a widely used alias of Volkoff's also meant that he was a severe security risk that needed to be taken care of. In this case, the only way to bring all the chips back into his possession would be to eliminate all loose ends which, unfortunately, meant that James had to be terminated.

James continued nervously watching the CIA agent pacing the length of the room, one hand gripping her suppressed gun and the other held up to her lips as she chewed on her thumb. He turned to look at Rebecca and saw her watching the scene with wide-eyed amazement and more than a little trepidation but James wasn't too worried about her. In his line of work, she was always the willing accomplice and he had taught her to fend for herself, at least as much as a girl her age could.

Turning back to Agent Frost, James wondered exactly what was going through her mind.

* * *

><p>After telling James Franco not to "freak out," Mary had decided that rather than proceed on what could be perceived as a rogue operation, she would try the official channels first. After all, it would be better for everyone involved if James was shuffled into WitSec rather than having to truly employ a Protocol Two on him, especially when the bombshell dropped that he was traveling the country and doing cons <strong>with his daughter<strong>, of all people.

She had very nearly smacked the man on the head for such a dimwitted way of raising a child before she bit her lip. Was she not being just a bit hypocritical? She had left her own family for long periods of time without so much as a by your leave and by now, her children had come to expect that she would be away and always expressed surprise, to varying degrees when she was actually around. It hurt her more than she cared to admit that her eldest was beginning to show signs of bitterness at the way she, not Mary, was left to tend to her younger brother and father.

Stephen was a wonderful man, there was no denying that, but he was certainly not without his faults. Amongst those faults was the fact that he adopted an extremely hands-off approach when it came to parenting. Mary had always been more involved but with her recently increasing amount of missions for Volkoff that had grown longer and longer in duration, Mary was not around much to temper Stephen's willingness to let the children raise themselves with some good old fashioned mothering.

Looking at James and his daughter, Mary felt another flash of anger at James. He was a perfectly normal human being with a college degree, for goodness sakes! Why was he traveling the country with a young girl and placing her in such danger just for a good adventure and a quick buck? And what about his wife and younger daughter, where did they fit into all this? There were so many unknowns that Mary felt momentarily overwhelmed by the situation.

Taking a deep breath, Mary employed one of the various calming techniques that she had picked up while at The Farm. She had to remain absolutely focus if she was going to be able to safe James and his daughter and, in spite of her training, she simply could not bring herself to kill a little girl for the greater good. If the greater good demanded the sacrifice of an innocent, what use was it to the people who needed it the most.

Mary willed away the doubts she was having about her job, she was good at it and it protected people and that was all she needed, for now at least.

Every face in the room turned to face the little table that stood between the two beds as the phone began ringing. Mary headed towards the phone quickly, shooting the nervous eleven-year-old what she hoped was a calming smile which she supposed worked because the little girl's frown shifted into a tentative and shy smile in return.

"Hello?" She breathed, unusually anxious as she held the receiver to her ear with both hands.

"May I speak to Ms. Hyde please?"

Mary breathed a sigh of relief at the seemingly innocuous question. It was the predesignated code phrase her superiors at the agency would use when establishing contact while in an un-secured environment. While the likelihood of the question being completely genuine was a possibility, Mary seriously doubted that providence would play such a cruel joke on her.

"This is she."

"Very well, Agent Frost, I have been instructed by the deputy director to relay your orders."

"I'm listening."

"Ascertain as to the authenticity of James Franco's account on his meeting with Alexei Volkoff, alias Greg Tuttle. All documents and monetary funds exchanged during the meeting are to be collected, cataloged and submitted for summary analysis. Once all information has been collected, you are to terminate James Franco as instructed by Alexei Volkoff and report for debriefing Langley at your earliest convenience. Do you understand your orders?"

"Wait, are you serious?" she turned to look at James who was hanging off her every word, leaning in closer as if he would be able to hear the speaker.

Motioning for James and Rebecca to briefly enter the bathroom, citing national security, Mary waited till she heard the click of the bathroom door closing before bringing the receiver back up to her ear.

"Agent Frost, are you still there?"

"Yes, sorry."

"Pertaining to your question, your orders are implicit. You are to terminate James Franco in any manner that you see fit."

"But what about his kid? Where's she going to end up?"

"It will be an unfortunate incident but I am sure she will find her way into the care of Child Protective Services."

"Franco's not even her real name, how are they going to be able to find her next of kin."

"The agency has already prepared sufficient documentation detailing the life of Rebecca Franco, native of Ohio, you need not concern yourself beyond this."

"I... I understand."

"Very well. Good morning to you Agent."

The dead tone soon filtered through the earpiece of the phone as Mary considered her options. The easiest thing that she could do was to follow her orders to a tee. Volkoff was unaware of the existence of Rebecca and, as such, was not expecting two dead bodies to lie in Mary's wake. The CIA's solution to the young girl was less than ideal but she would live.

_She would live but what would her life be like?_ _Would she ever be the same, knowing the way her father's life ended? Would she truly be safe from CIA reprisals? _The questions rose unbidden.

No, it was not acceptable. James Franco had cooperated fully thus far and except for being a good conman and a bad father, he was innocent and deserved to escape the crossfire of international intelligence mongering. It was not in Mary to disobey orders but for the sake of Rebecca who reminded her so much of her own children, she had no other choice. She was charged with protecting the people of the United States and she'd be damned if she played a hand in ending the life of one and, perhaps more devastatingly, ending the future of another.

Rubbing her face tiredly, she suddenly feel a bone deep ache that was wholly inconsistent with her extremely fit thirty-some year old body. The weariness, she realized, was bone deep and come from a totally non-physical source. The sacrifices the those in the intelligence community asked for was simply too high a price to pay but she was already in it, knee deep.

Standing from the bed she was sitting on, Rebecca's she realized, she made her way to bathroom door and pushed it open. Mary was immediately met with the sight of James lunging forward carrying what looked like... A plunger? Deflecting it easily, she twisted his right arm and turned him around before briefly kneeing the back of his knees, causing him to lose his balance. It was a simple feat to push him forward onto the ground after that fact.

"What the hell are you trying to do?" Mary hissed.

"I know what you're going to do!" James very nearly shouted. "You're going to kill me and then you're going to kill Rebecca!"

Mary looked up and around quickly, spotting the semi hidden in the bath stall defiantly brandishing a luffa, her posture indicating that she was ready to fight for herself and her father, if need be. Huffing at the situation, Mary couldn't help but be slightly impressed with both James and Rebecca for standing up to a trained killer.

"Rebecca, sweetie," Mary said softly, trying to calm down the girl. "I'm going to let your dad up now but I want you to promise that you won't attack me with that stick, okay?"

"How do I know we can trust you?" Rebecca questioned, her eyes narrowing suspiciously.

Smiling in spite of the situation, Mary lifted the gun from her coat pocket and, after making sure the safety was still on, ejected the clip and tossed it at Rebecca who caught it with surprising deftness, her other hand still firmly holding on to the luffa. Mary thought she looked downright hilarious but realized that perhaps laughing right now would not be the best course of action.

"Look, you have my bullets and I promise that I won't hurt either you or your father, deal?" Mary knew she could very easily disarm the girl if she wanted to but she was also loathe to inflict any sort of harm on the kid who, as Mary was quickly learning, was more than a little spunky.

Regarding the woman who was literally pinning her father down by sitting on his back, Rebecca considered the woman carefully. Nodding slowly and backing up just a bit, Rebecca motioned for Mary to release her father. Realizing a bit too late how ridiculous she must look brandishing a luffa at a CIA agent who was probably trained in over two hundred ways to kill a person, she lowered it to her side but did not relinquish her hold on it.

Mary made sure that she mad no sudden movements as she slowly got of James, grabbing hold of his arm to help him up. Once James was back on his feet, she backed away slowly from him and held up her hands, trying to show Rebecca that she was sincere.

When everyone had calmed down and settled back in the actual room with James and Rebecca perched on Rebecca's bed and Mary on James', Mary began outlining the details she thought they ought to know.

"Firstly James, I am terribly sorry but you have to die."

Mary cringed the moment she heard the words that came out of her mouth. _Perfect choice of words, _she thought and held up her hands quickly to forestall any outbursts coming from the tiny, fragmented family.

"That came out wrong," Mary apologized. "What I mean is Jack Burton must die."

"I'm not sure how that's different from seeing I have to die?" James frowned, wondering exactly what she meant.

"Okay, look at it this way," Mary began, trying to put words to the thoughts rampaging through her mind. "You and your daughter need to treat your real names like an identity. What do you do after you've move on to another con?"

"We shed our covers... Oh! You mean we need to shed all our known identities, including our real ones?"

"Something like that, it's a bit more complicated.

"Unfortunately, the CIA believes that you're a threat to the operation and must be terminated, at which point your daughter will be shuffled into foster homes, probably CIA sanctioned for the control of how she is made to think."

"So wait, the government wants me dead?"

"You've got to understand James, to the CIA, you're an obstacle into taking down what is quickly becoming the biggest thorn in their side which they've had little to no success at removing. I've been at this for quite a few years now and to leave a loose end in place could very well be a death sentence!"

"Okay, I understand that but it's still unnerving to know that our government has no qualms about killing innocent people..."

"I understand your concern and I'm frankly a bit shocked at it as well which is why I'm not going to follow my orders, otherwise you'd already be dead and a team would be here to make sure your daughter is... Taken care of."

"That still doesn't solve our problem," James said, indicating both Rebecca and himself. "Where do we go from here?"

"Here's the good news. I had a feeling things might come to a head and had my partner initiate something we call Protocol Two."

"Protocol Two? Sounds like something out of a science fiction movie."

"My husband is a bit of a nerd," Mary replied, her fondness clearly evident in her tone. "Anyways, Protocol Two is what we, that is my hus... um... partner and I use to take care of people. In this case, the two refers to people we don't know.

"This involves the creation of entirely new identities and it's fairly involved. This means new birth certificates, new names, new school records, new social security number, new everything. As you can imagine, the longer a headstand we have on the situation, the better since it's really a lot of base to cover."

"And you told your husband to prepare this for me before your orders came through?"

"Right, but the problem is I didn't know you had a daughter. I'm not sure if my partner was aware, he has a way of picking up information and forgetting to pass it along.

"Regardless, we'll be looking to relocate the two of you before the end of the day and it has to be kept completely off the books. I won't be able to stick around for much longer just in case my cover gets blown and I need to prepare for both of your deaths."

"I don't get what you mean."

"What I'm trying to say is, I'll be picking up a couple of unclaimed bodies and using them to stage a fake death for the two of you. After that, you'll move to a new secure location and keep out of the eyes of the law, both good and bad."

Mary stood up and covered the small distance between herself and James. Prodding him firmly in the chest with her finger, she stated as clearly as she could that this included no more hare brained get rich schemes and cons. After receiving a quick emphatic nod of agreement from James, Mary grabbed her purse off the bed and reached inside to grab her secure line to contact Orion.

"Orion secure."

"Frost secure."

"I've got most of the details ready for your mark."

"Please, please, please tell me you know that he's been traveling with his older daughter."

"Of course Mary, this is me. I've got almost everything prepared and ready to ship. Just need to insert these final transcripts into the UCLA mainframe and purge his records from the FBI database..."

"No go on the last, I'm going to make it seem like both of them died in an accident rather than making them vanish."

"Roger that... do you want me to change the blood type on their various records to match those of the bodies you'll be using?"

"That's a good idea, contact me when you're done with the information of the dead drop and I'll let you know what blood types I'll be using. I need to go get prepared on my end as well."

Mary hung up after trading quick goodbyes with Orion, knowing that she'd be hearing from him pretty soon anyways.

James and Rebecca were still huddled together on her bed when Mary set out to enact her part in the plan.

"Do not, and I repeat, do not open the door unless you're absolutely certain it's me. I'll use the code phrase 'now where are them keys' and you are not to contact anyone **or** use the peephole to verify identity, are we clear?"

"Crystal." James replied.

Satisfied, Mary left the room and quickly skipped down the eight flight of stairs to the lobby where she slipped out unseen into the dead of night. She had a couple of bodies to steal.

* * *

><p>Mary had been lucky. She found two suitable bodies soon after setting out in her search for replacements for James and Rebecca with Rebecca being the harder of the two to find a replacement for. Eleven-year-old girls were not often left unclaimed in the morgues of various hospitals located around the city but Mary had fortunately found a ten year old girl who, according to records, was killed in a car accident with her whole family. There would be no one coming to claim these poor souls.<p>

Parking the van that she had appropriated from a kind citizen, read stole, in an alley near James' hotel, Mary made her way into the underground parking area for guests rather than straight back up to James' room. Her planned required the car James was driving to erupt into a fireball and for that to work, she needed to rig a couple of wires and maybe nick the gas tank to ensure a proper fuel for the fireworks.

The final part of her plan was a bit more complicated and relied solely on human action. She wasn't sure it'd go off without a hitch but figured she could step in if required.

After being let back into the room, Mary made a last call to Orion to confirm that Protocol Two was a go, which it was. Making sure that both James and Rebecca were listening intently to her, she provided the two with the instructions they needed in order to slip into their new identities.

The first order of business was going to the local greyhound terminal and book a one way trip down to Omaha, Nebraska, where further instructions and documents awaited them in locker number seven. From there, they would utilize the car prepared for them and take the very long, very scenic route to Southern California. California was about as far the two could run while staying in the same country and the crossing of any border would leave too obvious a paper trail to cover, even with the technical know-how that Orion possessed.

Orion had also set up various bank accounts and a trust fund for Rebecca to ensure that even if something should happen to James, she would be well looked after. He had even managed to arrange for a house to be purchased in the new identity James would be using, paid in full using cash from a discretionary fund that had literally no oversight due to it's use in clandestine operations the world over.

The pair would be traveling light, carry little cash and small amounts of baggage so they would not draw any attention to themselves. When James had asked if he would be allowed to keep his money, a very firm no was his answer and Mary would've almost have sworn that a small pout appeared on his face for the briefest of seconds before a more somber expression replaced it.

Once Mary had double checked all the details and was certain that everything was in place, she dragged James aside for a quick chat.

"Look, you're being given a second chance at life and so help me, if you mess this up again, I will hunt you down and kick your ass."

"I know, I know, keep my head low and go about my business, don't stick out like a sore thumb."

"It's not just that, okay. Look, while you're here, taking your daughter for granted, certain people would kill for a chance to be there for them every step of the way. What about you? You're leaving her alone for hours at a time to do whatever it is she gets up to when you're not around and why? It certainly isn't because you need to provide for her!"

James was starting to get the feeling that Mary Frost wasn't exactly talking about him but he wouldn't stand for her questioning his methods, he had kept her clothed and fed through cons, after all.

"What? Of course it's to provide for her, how else am I supposed to get the money we need?"

"How about like a normal person, James? With a job. Look, I know you're no idiot, how often you manage to get away with cons is a testament to that and don't think I don't know about your college degree."

"Wha..."

"Look, all I'm saying is this; she's your daughter, do you really want her to grow up to live a life expecting constant disappointment knowing that she can never count on her dad for the things she needs and never knowing what a _real_ home is?" A pang shot through Mary at her own words and she felt tears welling at the corner of her eyes. Turning quickly so James wouldn't see her loose her composure, she made for the door mumbling some excuse or another.

James stared at the door as it closed with barely a sound, his mind churning over what Mary had just said. Would his daughter really grow up to expect nothing of him? He had been providing for her, after all, and it was she who decided to run off with him, not the other way around.

The simple fact, though, was that he wasn't ever really around even though he was _around_. Even when they were in the same car, they rarely ever spoke and James was always too busy planning his next con to actually just **be** with Rebecca. _Just how well do I even know her?_ James questioned himself_. I know her favorite ice cream... but what's her favorite color? Or her favorite song... does she even have one? What about her favorite book... My god, Mary is right!_

The sudden realization that he barely even knew his daughter struck him like a pile of bricks. She'd been with him for the last two years now and he barely knew anything about her. Thinking back to all their time spent together, James realized that he had treated his daughter more like shill than an actual family member and somehow, that made him sick to his stomach.

Mary was right, he was being given a second chance. He could do better... No, he **would **do better for his daughter, because if she didn't deserve it then who did? His thoughts flew briefly to his wife and younger daughter but James knew that his own actions had brought him to the point where he could no longer even hope to provide for them.

_Well wait, that isn't exactly true_, James thought. He had begun storing part of his scores away the moment Rebecca had joined him on his trip, something she could fall back on if anything happened to him. He was beginning to realize now that a hundred or so thousand was a poor substitute for a parent but maybe his wife and younger daughter would be able to use it. His wife was staying with her parents now and her father was a better than he had ever been and would provide for his family. The money would just go towards helping a bit, maybe a college fund for his other daughter.

Surprisingly, Mary allowed him to compose a letter to his wife detailing the location of his stash, even going so far as to suggest that he wanted to reconcile with them and bring Rebecca home. She admitted that it would hurt them when they received word that James and Rebecca were gone but if anyone were tracking their family, it would help keep them safer.

Once James had written his letter, he entrusted it into the care of Mary who promised she would mail it to his family the first chance she got.

Glancing down at her watch, Mary decided now was as good a time as any for the pair to depart. The earlier they got on the road, the more leeway she had with her part of the plan. Instructing James to leave everything except for about a hundred in loose notes behind, she stuck her head out into the corridor quickly to make sure no one was around before quickly ushering the two of them to the stairwell. Once safely ensconced in the stairwell, she gave father and daughter directions to the service entrance and bade them farewell before she turned to exit the stairwell and return to the room to clean up and wipe out any evidence that the pair were now on the run.

"Agent Frost," the voice stopped her, Mary turned around to look at Rebecca.

"Yes?" she asked her questioning look turning briefly to shock as Rebecca stepped up to her and wrapped both of her arms around Mary.

"Thank you." Rebecca whispered before quickly turning away and bounding down the steps.

Mary turned to look at James who wore a lopsided grin before he extended his hand. Reaching out her own hand to shake it, Mary was startled but pleased when she heard James speak.

"I thought about what you said and you were right. I'll try harder and I want to thank you for this chance."

"I'm glad you understood, now get going." as she watched James race down the stairs to catch up with Rebecca, Mary quietly uttered "Good luck." before pushing open the door to carry out her mission.

* * *

><p>Sirens blared up and down the street as onlookers watched with a morbid curiosity. It was just after eight in the morning when a car had seemingly lost control and veered straight into the wall of an apartment complex that was under construction. Witness later said that shortly after the impact, the car and its passengers erupted in a giant ball of flame with an loud boom.<p>

Mary watched from about a block away as a couple of fire crews attempted to put out the blaze that had expanded to the wooden frames of the new buildings that the car had crashed into. Police were all over taking statements from the witnesses who had seen the entire thing.

Pleased with the outcome, Mary turned away from the wreckage and made her way to a local payphone to report in to her CIA superiors. She had barely slipped a quarter into the payphone when her special wireless phone began to beep, indicating a call from her partner.

"Frost Secure."

"Mary, you've got to run."

"What are you talking about Stephen?" her worry was evident, Stephen rarely broke from protocol, even if the phones they were using were untraceable by anyone.

"The CIA has issued a burn notice with your name on it, you've got to get out of there!"

"Why would they do that?"

"I don't know but until I can figure this out, we need to go dark. I'm going to begin purging all my records, there isn't anyone else except you that's worked with me and seen me personally, I should be safe once I purge everything."

"But what about me? What am I supposed to do?"

"I hate to say it Mary, but it looks like Volkoff is safest place for you to be right now. With your burn notice, it solidifies your position in his ran... Son of a bitch!"

"What, what is it?"

"According to the filing, the order came from the Office of the Deputy Director of Operations. Reasons cited including carrying out an unsanctioned assassination on US soil and directly countermanding orders to bringing in a witness."

"What the hell? I haven't even reported in and the last time I checked, my orders were to terminate James Franco!"

"Let me pull up the order filing itself..." Stephen said. A minute later, he sighed and his heart sank. "You've been played Mary, there are no official order filings on the book."

"Are you absolutely certain Stephen? I mean maybe it hasn't been put into the system yet." but Mary knew better. These things were filed almost immediately because the central computer server hub located at Langley was accessed daily by analysts and station chiefs around the world.

"I'm not sure Mary but I don't like this one bit. I want you to run and don't you dare look back until this whole thing is sorted out."

"Stephen, the children..."

"Can look after each other! And how far behind will the CIA be if you lead them straight to us?"

"You're right but damn it, Stephen, they're just kids! Ellie is only fourteen and she **cannot** be expected to be looking after Chuck alone!"

"I'll take care of it, you... you just get yourself out of the country as soon as you can. And Mary,"

"What is it Stephen?"

"I want you to swing by the Cleveland dead drop and pick up the pair of sunglasses I left inside the vault."

"Why are a pair of sunglasses so important that I'm risking making a detour while on the run from the CIA?" she asked, truly curious as to his reasoning.

"They're more important than you can ever know. Just, just get them and hold on to them for now, I'll be in touch... I love you."

"I understand and I love you too, please look after the kids while I'm gone."

"Just, promise me you'll come back."

Mary brought the phone to her chest for a brief moment, steeling herself because she knew it would be a lie. With the CIA putting a sanction on her, there was no telling when she would, if ever, be able to sort out the mess that this had created. The fact that the sanction came from the office of one of the most powerful men in the agency would only make it ever more difficult.

Quickly wiping away the tears, Mary brought the phone back to her ear as she dumped the rest of her possessions into the trash and whispered.

"I'll be back."

* * *

><p><strong>Los Angeles, California - Two weeks later.<strong>

"Well Darlin', what do you think of your new home?" he asked, his arm wrapped warmly around her shoulders as the two of them looked around the empty living room, peering around at what would be their new home, the first in a good long while.

"It looks nice... You're really not going to run anymore, are you?" Long conversations held along the road trip to California had brought to light the many insecurities she had about her father, how she was always wondering if he would be there when she woke up or whether he would come back and, at the root of it all, how he _had_ left her. True, that was when she was much younger and she still lived with her mother and younger sister but his leaving without a word had hurt her deeply.

They had come a long way the last two weeks towards reconciliation but it would take awhile yet before she got over years of living through her deepest fears. He felt even more ashamed than he already was. He was her father, after all, and it was his job to keep her from getting hurt yet he was the single biggest cause of hurt in her young life thus far. He vowed to himself again that he would change, he had to.

"I promised I'll change and this is one promise I plan to keep, Darlin',"

Before she could reply, a knock on their front door made the both of them turn around to regard the man who was a bit on the short side wearing a blue and white flannel shirt tucked into neatly into pressed tan slacks. He was smiling widely at them though they both could see the sadness and pain in his eyes.

"Welcome to California," the man said. "It's good to meet you Jack and Sarah, my name is Stephen Bartowski."

_End of Choices Arc._

* * *

><p><strong>AN:** Well, there you have it, the wrap up to the initial arc that sets the stage for different meetings between the people, I hope you enjoyed it and if you did or if you see some kind of factual or grammatical error, please don't hesitate to let me know so I can go back and fix it. As I said in my first author's note, I'm taking some liberties with the time-line which include when Mary went rogue.

That said, I've received quite a bit of feedback on **vs. the Reassignment** about people wanting me to continue it and I will admit, it was a little overwhelming because it was just an idea I had while doing some research for this story. I've been very reluctant to spend any time on it due to something that I have to do in the near future that will put a severe cramp on the amount of time I will be able to devote to any writing but I have decided that I will at least expand a bit on the storyline as well as continue it beyond where it stands now.

I would like to especially thank **uplink2** for his thoughts on the matter because it did give me the perspective of looking at it as both a writer and a reader. As a writer, I was _mostly_ content to let it stay the way it is but as a reader, which I've been far longer than I have been a writer, at least of fanfiction, I can understand the frustration of reading a story that basically ends in a cliffhanger (Season 2 anyone?) so I'm going to rectify that.

Other than that, thanks once again for reading and please review if you liked it (or didn't, so long as no flaming is involved and constructive criticism is offered).

Cheers.


	4. Bondes Forged, Part One

**A/N: **So, here it is, Chuck and Sarah, together again. Except they aren't. I had a lot of difficult writing this because I have absolutely no clue if any of what I've written makes sense from an American point of view. I tried to leave certain aspects I really have no idea about as vague as I could but I apologise if there are any mistakes. Don't hesitate to tell me if something isn't right and I'll try and fix it, thanks.

**Disclaimer: **I do not own Chuck.

* * *

><p><strong>Chapter Four: Bonds Forged, Part One.<strong>

**September 1994.**

The halls were filled with the loud chatter of teenagers talking about everything under the sun as the milled around, waiting for the bell to ring. Sarah navigated through the sea of people as she felt a near panic welling up inside of her.

It had been two and a half years since CIA Agent Mary Frost had come into her life and changed the course of it and Sarah could honestly say that she was extremely thankful for it. In the last couple of years, she and her father had gotten much closer with Sarah being able to air a lot of her insecurities with him and he had done an admirable job of always being there for her.

It had taken a lot of getting used to, initially, both having her father around all the time and being in a real home without having to consider moving at a moment's notice. The last time Sarah had truly lived in a home was with her mother and sister but even then, her father had always been an absent member. Now, the roles were reversed and Sarah felt herself highly conflicted. While she liked the fact that she and her father had settled down, she had never actually _lived_ with him before and it took a bit of getting used to

She also found herself missing her mother and sister fiercely and had been known to ask her father on multiple occasions if they would ever meet with them again. While he had been evasive, Sarah always knew, deep down, what he really meant and it had made her mopey for the first few months. She had never had this issue before due to that fact that, while on the road, it often felt like they were still moving and would one day move back to the rest of their family.

Sarah also had to adapt to not having a new place to explore like she usually did when her father had left her behind while going off to pull his latest con. During those times she was left alone, she would often wander about the neighborhood where the motel was located, even if it was a bit seedy. Now that she was in an actual house, in an actual neighborhood, Sarah found it a tad boring, she had to admit.

Still, Sarah was nothing if not adaptable, the way she managed to get into the life of the wandering adventurer with her father had proved that much. It had taken a few months but Sarah had finally managed to settle down into a routine. The fact that she was to be home schooled till the year she entered junior high both helped and hindered Sarah's acclimation. On the one hand, Sarah had learned to be a loner and with nothing to restrict her schedule, she could learn to acclimate on her own time. On the other hand, she had and would spend years without anyone to talk to for any length of time except her father and that had helped to further foster her loner personality.

During those years where she had mostly stayed at home, she occupied herself by fully engaging herself in academia. She blazed through the coursework for the two years that she had missed with nary a slowdown and had proceeded to assimilate as much of the schoolwork that the two years she was missing had to offer. Her father had often told her to take it easy, that she had all the time in the world and that was what Sarah was afraid of. She had so much time that she really had no idea how to spend it, which was why she spent so much of her time reading and studying.

Things finally changed for her one warm summer's day, a couple of months before she started junior high, when she was taking a stroll through the park with her father at home settling some banking matter or another that was yet another facet of their fake, real life. She was almost out of the park when she heard shouts and the unmistakable sound of a fight. Curiosity getting the better of her, she had gone off to investigate and found a couple of tall-esque boys taking turns tormenting a really tiny kid. Sarah's first thought was that they were bullying a much younger boy but on closer inspection, she noticed that he was just generally small in stature.

Not knowing what to do about the situation, Sarah continued watching from a distance, also looking about to see if there were any grown ups who could break up the fight. A sudden thought occurred to her when she spotted an abandoned soccer ball about midway between her and the three boys. _Probably belongs to them, _she thought. Figuring that it would be of little consequence, Sarah took a short running start and kicked the ball in the general direction of the boys. What she had not been expecting was the smooth nearly straight line the ball took as it sailed through the air, over the adjacent path and straight into the head of one of the boys.

An surprised and angry shout sounded out from the group and all three swung their heads to look at Sarah who had the typical "caught in the headlights" look. When the two larger boys made a move towards her, she did the only thing that she could think of and took off in a sprint. The shouts continued for awhile but Sarah had long forgotten all about her pursuers, her mind focused solely on how good it felt to have the wind in her face.

It was from that day on that Sarah would often take an hour or so out of her day to just run for the sake of running. The fact that it helped build up her physical strength was just an added bonus.

She snapped out of her thoughts when she heard the first warning bell go off, as groups of kids started making their way to various classrooms, Sarah hurried along with them, making it into one of the last seats in her class before the second bell rang.

It was a couple of minutes later, right in the middle of the teacher's lecture how they were in junior high now and that it was no longer fun and games, when the door creaked open and a tall, lanky teen tried to sneak in to the best of his ability. That is, until he realized everyone in the room, including the teacher, was staring at him. The boy seemed to snap to full attention, Sarah's eyes going wide as he kept going up and up... and up. While she was tall herself, for her age, the boy's extremely lanky height and coupled with the fact that she was sitting, he looked unnaturally tall.

"So glad you could join us mister..." their homeroom teacher, a Mr. Rangvalder, middle-aged, portly and wheezed in a nasally tone, said to the new comer, fishing for his name.

"Er, um, Chu... Charles Bartowski." the boy replied.

Sarah shot up in her seat immediately at hearing the name. The man who had introduced himself that very first afternoon Sarah and her dad had arrived at their new home was a Bartowski as well. He seemed like a nice man, even if he spoke a bit too quickly and seemed to have a nervous twitch, he had always been kind to her, making her smile and asking her to call him Mr. B.

"Not a very good impression to make on the first day Mr. Bartowski," Rangvalder intoned, his nasally voice irritating Sarah more by the minute.

"Oh! Um, yes... er, I'm sorry but there was a sort of emergency at home. You see my sister kind of forgot her..." he droned on, obviously rambling. Sarah was seated in the front row so she couldn't see behind her without turning around but she swore she could match the snickers that were floating around behind her to the expressions of her classmate's faces.

"Yes, yes, I'm sure it's fascinating. I'll let it slide this once because it's the first day but I'm watching you, Bartowski."

"Yes sir." the boy who had introduced himself as Charles muttered out before plopping himself down in the nearest empty seat, right next to her.

By the end of homeroom, there were one thing Sarah was absolutely certain about. One, Mr Rangvalder was the most annoying human being she had ever met. His constant nasally twang was already enough to set her on edge but the fact that he could not stop extolling on how every one of the miscreants, meaning her fellow classmates and herself, were always up to no good and that he'd make sure that every one of them behaved up the expectations of the school had her gritting her teeth. Her father and Mr. B had told her to not stick out and she was trying her best not to but something about the man just rubbed her the wrong way.

She offered up a silent prayer when homeroom ended, about ten minutes later.

As the class was exiting the room, she hung back for a brief moment to watch her various classmates filing out of the room and she noticed, a large part through their body language, that many of the students had either ignored Rangvalder or taken it in stride, the only exception being Charles. He seemed a bit perturbed, though Sarah could easily understand why. Each time Rangvalder had made a comment about first impressions and rule breaking, Rangvalder had glanced at Charles, singling him out. Sarah bristled at that, she hated bullies in any shape and form.

Realizing she would be late for her first class if she continued to just wait out everyone leaving, she joined the throng of students who dispersed to their various classes. Sarah herself was headed to elementary algebra, her hours of studying at home paying off. When she had first enrolled in the school, officials had decided that she needed to take placement tests to see where she stood in her level of competence and Sarah had tested into a lot of higher level classes, something she was immensely proud of.

Once again being amongst the last students in class, Sarah quickly took a seat in the front row moments before the class started. She was a bit startled when she realized her neighbor on the left was none other than Charles Bartowski. From the comments made by the teacher throughout class, she soon learned that Charles, herself and one other were the only seventh graders in the class, everyone else being an eight grader.

If she was completely honest with herself, Sarah would admit that she was a bit nervous about school. She had worked well on her own for so long and going to school again was such a new experience for her that she felt a bit out of control. While on the run with her father and even after they had settled down, so much of what she did was dictated by no one other than herself with a timetable that she alone set, except when they were traveling to a new place.

Taking a deep breath, Sarah pushed down her nervousness and turned back to the class. It soon became apparent that while she was smart, Charles was something else entirely. Any of the supplemental questions their teacher threw out, he was always the first to solve and answer with Sarah being a bit slower than him. The competitiveness in her flared up at that but despite her best efforts, Charles just seemed so much better at algebra than she was. It didn't mean she was a slouch, by any measure, he was just that much better

By the end of the period, almost everyone was looking at the lanky kid with something akin to awe and disbelief, though Sarah was not deaf to the faint murmur of complaints as a younger student showed up many of the older students. Scowling to herself at fragile egos, she ignored the whole lot as she went about her way for the rest of the day. Excitement at this new adventure called school now overshadowing her nervousness.

* * *

><p>At dinner that night, Sarah couldn't help but bring up the topic of the lanky math genius who shared a same last name as Mr. B at meal that was home cooked, something her dad had been working on since settling down. He had tried to recreate many of her favorite dishes from back home early on, experimenting with ingredients and techniques, but his skills in the kitchen had been terrible, at best. After their first disastrous home cooked meal which involved way too much fire extinguisher, he had taken it upon himself to learn to actually cook before attempting to experiment.<p>

As Jack was doling out a generous helping of steamed vegetables onto Sarah's plate, she asked the question that had been plaguing her all day.

"Dad, does Mr. B have kids?"

"Erm... yes he does, Darlin', why do you ask?" Jack replied, slightly surprise at the topic of the conversation.

"I think I kind of met his son today, at school."

"How do you 'kind of meet' someone, anyway?" he asked, smiling slightly.

"He was late to homeroom and he was really tall, much taller than Mr. B. He was in my algebra class as well. Seems super smart, beat me on every single question we had in class." Sarah said, pouting slightly at the last part.

"Now Darlin', you know what I always say. If you're good at something, there's bound to be someone that's better."

"I know, I just don't like losing."

"A bit of healthy competition is fine," Jack said, winking at her. "Just make sure you don't bring it to fair."

"I know."

"That's good, now don't think I don't notice you picking out the peas."

Sarah's answering smile was such a perfect mix of mischievousness, cunning and innocence that Jack could not help but let out an uproarious laugh.

* * *

><p>While in many of the same classes as well as homeroom together, Sarah and Charles had not officially met and had barely traded more than a handful of words with each other since the start of the school year.<p>

It was a couple of weeks later that Sarah and Charles's life collided with one another, literally. She had been coming round the bend in a hurry, having been a bit slow to wake that morning despite her dad's best attempts at waking her and he had come around from the opposite direction. The result was a veritable eruption of papers, books and teenagers. Sarah picked herself up from where she had landed on the floor and saw Charles sprawled out, his limbs seemingly everywhere.

Seeing him in such an awkward position, Sarah had to clap a hand over her mouth to muffle the sudden guffaw that threatened to break out. Squatting down quickly, she began gathering up her notes and books while Charles rearranged his mass of limbs and helped her as well.

"Sorry about that, I forgot one of my books and class is about to..." the bell ringing in the background made them both groan. They were officially late now and Rangvalder would most assuredly not let them hear the end of it. "Start." he finished lamely.

"Rangvalder's going to be pissed." she moaned, voicing both their thoughts.

"Yea, he really is going to be. You better head on ahead, I don't want to get you into any more trouble than you already are."

"Right, good luck to us both," Sarah said as she quickly resumed her trek to class.

Charles watched her walk away for a few seconds before shaking himself out of his reverie. Rangvalder was already going to have his head for being late, no point in pushing the envelope further by being even later than he already was.

In the end, both Sarah and Charles landed up with a detention a piece which would be served out at the end of the day. While Charles was lamenting his bad luck, Sarah was far more interested in the news that the girl's track team would be holding tryouts later in the week and she really hoped that the detention wouldn't coincide with the tryouts. It was the first time she had heard of the school's track team but, she reasoned, any reason to do more running was a good thing.

Detention, as it turned out, would be served at the end of the day and Sarah found that she was genuinely upset at having to serve it. _It's all Charles's fault, _she reasoned. _If he hadn't knocked me over, I wouldn't have been late._ That train of thought persisted till detention period and she found herself quite angry at the Bartowski kid. Deep down, Sarah knew it was completely irrational but at the moment, she was completely happy to pin the blame on him.

When she walked into the classroom that was being used for detention, Sarah found that the only other person there was Charles. Making sure to take a seat as far away from him as possible after signing in, Sarah continued to stew at her unjust punishment as she pulled out some of her math assignments to work on. She decided that even if she was here unjustly, she might as well make the best of a bad situation.

She was so focused that she didn't realize that the thirty minute detention was over and that the overseeing teacher had already left.

"That's not the right way to do it, you know."

The sudden comment made from directly in front of her desk caused her to jump.

"What?" she asked, failing to keep the annoyed tone out of her voice.

"Woah, there," Charles said, holding his hands out in front of him as if to ward her off. "I just came over to tell you detention is over since you were so engrossed and I noticed you substituted a variable wrongly."

Looking through her work, Sarah noticed her error but her annoyance at Charles only grew as her competitiveness took over.

"Yeah, I see it," she let out dismissively.

"Just trying to help," he mumbled out dejectedly as he left. Truth be told, he had been intrigued by the girl since his best friend had pointed her out, the very first day of class. Morgan had been regaling him with tales of the girl who had saved him from two bullies he had accidentally angered after mouthing them off ever since the summer and Chuck was beginning to believe she was a figment of his over active imagination.

Morgan had been upset, at first, when he found out that he was in a different homeroom than Chuck and that Chuck would be engaging in far more advanced classes than he, himself would. Chuck had calmed him down by suggesting that they meet often during the small breaks between classes. It was during the first of many meet ups that Morgan had first spied Sarah. Chuck had already left the algebra classroom and was idly chatting with Morgan when he suddenly grabbed hold of Chuck's sleeve, tugging at it incessantly.

"Dude, dude, dude, that's her, right there!" he had said, pointing at Sarah without a shred of subtlety, excitement coloring his tone. "That's the girl who kicked the ball straight into that douche bag's head! And man, you should have seen her run. It was like the Flash, only slower and a girl."

Chuck smiled as he listened to his friend's enthusiastic comments, glad that the girl was oblivious to Morgan's gesturing, while taking a good look at her and it was then that he realized it was the same one that he had spent homeroom and the last class sitting right next to. The first thing that struck him about her was her height. He was already really tall for his age, standing at five feet seven inches but she wasn't much farther behind, he estimated maybe five feet three inches. She was easily the tallest girl around. The second thing he noticed about her was her eyes, the a deep blue that seemed so guarded.

Shrugging his shoulders at Morgan, the two walked a ways down the corridor together before separating off into different classes. Chuck was only partially surprised to see the girl there again, this time paying attention to try and pick up her name. It had not taken long before he learned that her name was Sarah Walker and that she was really smart but that she was also a loner, seemingly a bit awkward at social interactions.

Seeing Charles walk out of the room, his shoulders slumped, Sarah couldn't help but feel bad at the way she had treated him. Gathering her things quickly, stuffing her books unceremoniously into her bag, she rushed out after him.

"Charles!" she called to his retreating back, making him turn around to see who was calling him.

Rushing right up to him, Sarah swallowed nervously, feeling extremely awkward and uncomfortable at having to interact with other people. She had spent so many years without having to really associate with others that her communication skills were probably severely lacking.

"Um, look," she stuttered, cursing herself as a blush bloomed on her face. "I just wanted to say I'm sorry, I shouldn't have snapped at you back there."

Charles regarded her for about a minute, Sarah fidgeting under his gaze, before he finally replied.

"Chuck."

"I'm sorry?" she replied, puzzled by what he had just said.

"My friends call me Chuck," he clarified, before sticking out his hand.

Sarah stared at the hand he was holding out to her for a long minute, wondering at the implications. She had often observed as her father lured many a mark in, all starting with the handshake and she wasn't totally sure what it was meant to represent. Sarah **knew **it was meant to represent an introduction of sorts, a friendly gesture. Charles had said his _friends_ called him Chuck._ Does that mean he wants to be friends?_ Sarah asked herself mentally.

Chuck was starting to feel a bit out of place with his hand stuck out in front of him as the girl continued to look at his hand like it was some kind of foreign, alien appendage. He was about to pull back when her hand shot out and firmly shook his.

"Sarah Walker." she said firmly, resolving in her mind that it didn't matter what her father had used the gesture of a handshake for, Sarah was going to remember it as the first step she took into making friends again.

_To be continued..._

* * *

><p><strong>AN:** Hoping people will start enjoying this fic more now that I've introduced both Chuck and Sarah as the focus of the story. I had a lot of trouble making the names make sense when focusing on the different characters, so I hope it isn't too confusing. Also, now that I look back through it, this is probably the first time I've written a chapter without some kind of reference to pop culture or Chuck, at least none that I can think of. As always, please let me know what you think.

Cheers.


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